Header list of 1k8l.pdb file
Complete list - 19 20 Bytes
HEADER DNA 24-OCT-01 1K8L
TITLE XBY6: AN ANALOG OF CK14 CONTAINING 6 DITHIOPHOSPHATE GROUPS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: FIRST STRAND OF CK14 DNA DUPLEX;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: DITHIOATED AT T10, C11;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES;
COMPND 7 OTHER_DETAILS: CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: SECOND STRAND OF CK14 DNA DUPLEX;
COMPND 10 CHAIN: B;
COMPND 11 FRAGMENT: DITHIOATED AT G17, C22, C24, G27;
COMPND 12 ENGINEERED: YES;
COMPND 13 MUTATION: YES;
COMPND 14 OTHER_DETAILS: CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE
SOURCE 4 CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY;
SOURCE 5 MOL_ID: 2;
SOURCE 6 SYNTHETIC: YES;
SOURCE 7 OTHER_DETAILS: SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE
SOURCE 8 CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY
KEYWDS XBY6, CK14, CK1, PHOSPHORODITHIOATE, NF-KB, DNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR D.E.VOLK,X.YANG,S.M.FENNEWALD,D.J.KING,S.E.BASSETT,S.VENKITACHALAM,
AUTHOR 2 N.HERZOG,B.A.LUXON,D.G.GORENSTEIN
REVDAT 4 22-JUN-22 1K8L 1 REMARK
REVDAT 3 23-FEB-22 1K8L 1 REMARK LINK
REVDAT 2 24-FEB-09 1K8L 1 VERSN
REVDAT 1 15-APR-03 1K8L 0
JRNL AUTH D.E.VOLK,X.YANG,S.M.FENNEWALD,D.J.KING,S.E.BASSETT,
JRNL AUTH 2 S.VENKITACHALAM,N.HERZOG,B.A.LUXON,D.G.GORENSTEIN
JRNL TITL SOLUTION STRUCTURE AND DESIGN OF DITHIOPHOSPHATE BACKBONE
JRNL TITL 2 APTAMERS TARGETING TRANSCRIPTION FACTOR NF-KAPPAB
JRNL REF BIOORG.CHEM. V. 30 396 2002
JRNL REFN ISSN 0045-2068
JRNL PMID 12642125
JRNL DOI 10.1016/S0045-2068(02)00510-2
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : MORASS 2.5, AMBER 5
REMARK 3 AUTHORS : GORENSTEIN (MORASS), CASE,KOLLMAN, ET AL (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 DISTANCE RESTRAINTS WERE DERIVED BY MORASS 2.5 USING A TOTAL
REMARK 3 RELAXATION
REMARK 3 MATRIX APPROACH.
REMARK 3
REMARK 3 AMBER 5 WAS USED FOR MD AND MINIMIZATION. THE DEPOSITED STRUCTURE
REMARK 3 REPRESENTS
REMARK 3 THE AVERAGE OF TEN FINAL STRUCTURES
REMARK 4
REMARK 4 1K8L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-01.
REMARK 100 THE DEPOSITION ID IS D_1000014695.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278; 288
REMARK 210 PH : 6.7; 6.7
REMARK 210 IONIC STRENGTH : 100 MM; 100 MM
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1 MM DUPLEX, 12 MM NA2HPO4, 8 MM
REMARK 210 NAH2PO4, 56 MM NACL, 50 UM NAN3;
REMARK 210 1 MM DUPLEX, 12 MM NA2HPO4, 8 MM
REMARK 210 NAH2PO4, 56MM NACL, 50 UM NAN3
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : AMBER 5
REMARK 210 METHOD USED : MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 10
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK:
REMARK 210 THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR
REMARK 210 TECHNIQUES.
REMARK 210 PROTON RESONANCES WERE ASSIGNED USING COSY, TOCSY, AND NOESY DATA
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 HO5' DC A 1 OP2 DC A 2 1.40
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 DC A 1 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES
REMARK 500 DC A 1 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES
REMARK 500 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES
REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DT A 9 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DG B 15 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DA B 19 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DT B 23 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DT B 23 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES
REMARK 500 DG B 28 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1K8J RELATED DB: PDB
REMARK 900 NMR STRUCTURE OF CK14, THE NON-THIOATED ANALOG OF XBY6
REMARK 900 RELATED ID: 1K8N RELATED DB: PDB
REMARK 900 NMR STRUCTURE OF CK14, AN ANALOG WITH 2 PHOSPHORODITHIOATES
DBREF 1K8L A 1 14 PDB 1K8L 1K8L 1 14
DBREF 1K8L B 15 28 PDB 1K8L 1K8L 15 28
SEQRES 1 A 14 DC DC DA DG DG DA DG DA DT T2S C2S DC DA
SEQRES 2 A 14 DC
SEQRES 1 B 14 DG DT G2S DG DA DA DT C2S DT C2S DC DT G2S
SEQRES 2 B 14 DG
MODRES 1K8L T2S A 10 DT THYMIDINE-5'-DITHIOPHOSPHORATE
MODRES 1K8L C2S A 11 DC CYTIDINE-5'-DITHIOPHOSPHORATE
MODRES 1K8L G2S B 17 DG GUANOSINE-5'-DITHIOPHOSPHORATE
MODRES 1K8L C2S B 22 DC CYTIDINE-5'-DITHIOPHOSPHORATE
MODRES 1K8L C2S B 24 DC CYTIDINE-5'-DITHIOPHOSPHORATE
MODRES 1K8L G2S B 27 DG GUANOSINE-5'-DITHIOPHOSPHORATE
HET T2S A 10 32
HET C2S A 11 30
HET G2S B 17 33
HET C2S B 22 30
HET C2S B 24 30
HET G2S B 27 33
HETNAM T2S THYMIDINE-5'-DITHIOPHOSPHORATE
HETNAM C2S CYTIDINE-5'-DITHIOPHOSPHORATE
HETNAM G2S GUANOSINE-5'-DITHIOPHOSPHORATE
FORMUL 1 T2S C10 H15 N2 O6 P S2
FORMUL 1 C2S 3(C9 H14 N3 O5 P S2)
FORMUL 2 G2S 2(C10 H14 N5 O5 P S2)
LINK O3' DT A 9 P T2S A 10 1555 1555 1.62
LINK O3' T2S A 10 P C2S A 11 1555 1555 1.62
LINK O3' C2S A 11 P DC A 12 1555 1555 1.62
LINK O3' DT B 16 P G2S B 17 1555 1555 1.62
LINK O3' G2S B 17 P DG B 18 1555 1555 1.62
LINK O3' DT B 21 P C2S B 22 1555 1555 1.62
LINK O3' C2S B 22 P DT B 23 1555 1555 1.62
LINK O3' DT B 23 P C2S B 24 1555 1555 1.62
LINK O3' C2S B 24 P DC B 25 1555 1555 1.62
LINK O3' DT B 26 P G2S B 27 1555 1555 1.62
LINK O3' G2S B 27 P DG B 28 1555 1555 1.61
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
Complete list - 19 20 Bytes